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[188500_at] collagen

Description T15B7.4 /REP_DB=WormBase Gene ID /WP=CE13654 /TR=O17036 /GB=AAB69961.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_high1_10_10 > 91      6grp_total > 93      4grp_total > 57      6grp_cgc > 98      6grp_high1_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 781
1 2 3 4 range
A 88.8
(-2.4)
A 		695.5
(2.3)
P 		785.9
(3)
P 		5.1
(-3)
A 		781
B 43.8
(-2.6)
A 		599.2
(2.6)
P 		637.8
(3)
P 		5.1
(-3)
A 		633
C 83
(-2.3)
A 		612.5
(3)
P 		605
(2.9)
P 		8.9
(-3)
A 		604
avr 71.9
(-2.4) 		635.7
(2.6) 		676.2
(3) 		6.4
(-3) 		670

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 903
1 2 3 4 5 6 range
A 184
(-2.7)
P 		355.2
(-1.4)
P 		289.9
(-1.9)
P 		600.1
(0.5)
P 		920
(3)
P 		146.9
(-3)
P 		773
B 266.6
(-2.5)
P 		328.3
(-2)
P 		421.1
(-1.3)
P 		417.3
(-1.3)
P 		942.5
(3)
P 		209.1
(-3)
P 		733
C 217.6
(-2.5)
P 		317.3
(-1.8)
P 		326.9
(-1.7)
P 		453
(-0.9)
P 		1040.3
(3)
P 		137.5
(-3)
A 		903
avr 222.7
(-2.6) 		333.6
(-1.7) 		346
(-1.6) 		490.1
(-0.6) 		967.6
(3) 		164.5
(-3) 		803
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 210
1 2 3 4 range
A 32.3
(-2.1)
A 		151
(1.4)
P 		205.4
(3)
P 		0.8
(-3)
A 		205
B 14
(-2.5)
A 		148
(3)
P 		147.8
(3)
P 		1.1
(-3)
A 		147
C 27.5
(-2.3)
A 		176.1
(2)
P 		210.9
(3)
P 		1.5
(-3)
A 		209
avr 24.6
(-2.2) 		158.4
(2) 		188
(3) 		1.1
(-3) 		187

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 349
1 2 3 4 5 6 range
A 33.9
(-3)
P 		126.3
(-0.7)
P 		63.1
(-2.3)
P 		152.2
(-0.1)
P 		277.6
(3)
P 		35.8
(-3)
P 		244
B 92.8
(-2.7)
P 		109.3
(-2.4)
P 		102.2
(-2.5)
P 		110.5
(-2.4)
P 		382.9
(3)
P 		78
(-3)
P 		305
C 80.7
(-2.3)
P 		96.8
(-2)
P 		83.2
(-2.2)
P 		91.1
(-2.1)
P 		336.6
(3)
P 		46
(-3)
A 		291
avr 69.1
(-2.7) 		110.8
(-1.8) 		82.8
(-2.4) 		117.9
(-1.6) 		332.4
(3) 		53.3
(-3) 		279
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188500_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11323
Sequence Type Exemplar sequence
Representative Public ID T15B7.4 NCBI
Target Description T15B7.4 /REP_DB=WormBase Gene ID /WP=CE13654 /TR=O17036 /GB=AAB69961.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_072335(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072335 NCBI Caenorhabditis elegans T15B7.4 (collagen) mRNA, complete cds. 11/11 None
SNAP00000035388 ENSEMBL cdna:SNAP chromosome:CEL140:V:6833780:6834806:1 11/11 None
GENEFINDER00000035395 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:6833780:6834806:1 11/11 None
T15B7.4 ENSEMBL cdna:known chromosome:CEL140:V:6833780:6834845:1 gene:T15B7.4 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:6833780-6834807(+) 87.32 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-142
Ensembl T15B7.4
Entrez Gene 188514 Entrez gene
SwissProt O17036 EMBL-EBI
WormBase CE13654 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6817 phosphate transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5737 cytoplasm inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
42302 structural constituent of cuticle inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB69961 Collagen protein 142 [Caenorhabditis elegans] ref|NP_504736.1| T15B7.4 [Caenorhabditis elegans] 1.0E-44
blast AAB69959 Collagen protein 143 [Caenorhabditis elegans] ref|NP_504738.1| T15B7.3 [Caenorhabditis elegans] 1.0E-43
blast CAE71959 Hypothetical protein CBG19029 [Caenorhabditis briggsae] 2.0E-43
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 8.0E-28
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.8E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504736.1 1 7-29
T15B7.4 1 7-29
SNAP00000035388 1 7-29
GENEFINDER00000035395 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188500_AT
ggagcaagaatcaacccagctaccggaagaccaggattctgcatcacttgcccagcagga
gcaccaggaccagctggaccaccaggagccccaggaccaaagggtaacaacgggcaacca
ggagccccagctcaatccggaggacgtggaccaccaggaccacgcgggccagccggagat
gccggatcaccaggacagccaggacacccaggatcgccaggaaacccaggacgtggagga
caacgaagccgtggacttccaggaccatcaggaagaccaggaccaccaggaccagctgga
ggaccaggacagccaggacactccggaggagcaggatctccaggtccacaaggaccacca
ggaccatccggacaaccaggacattctggaaacgacggagttccaggagcaccaggaaac
ccaggatccccaggaggagatgccgcctactgcccatgtccagctcgttcagctgctatt
gctgctcgttccagagttgccgcccgttcccgtgtcgctgctcgttcccgtgttgttgct
cgttctcgcgtcgtggctcgcaatcgtgttgccgccaagagacgtgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGCAAGAATCAACCCAGCTACCG 373 519 364 Antisense
CCAGCTCAATCCGGAGGACGTGGAC 648 271 490 Antisense
GGACGTGGAGGACAACGAAGCCGTG 299 75 592 Antisense
AGGACAACGAAGCCGTGGACTTCCA 353 55 600 Antisense
CAGCCAGGACACTCCGGAGGAGCAG 276 203 673 Antisense
GACACTCCGGAGGAGCAGGATCTCC 265 367 680 Antisense
TCCGGAGGAGCAGGATCTCCAGGTC 211 593 685 Antisense
CATGTCCAGCTCGTTCAGCTGCTAT 565 209 818 Antisense
AGCTCGTTCAGCTGCTATTGCTGCT 655 79 825 Antisense
TCGCAATCGTGTTGCCGCCAAGAGA 480 599 921 Antisense
ATCGTGTTGCCGCCAAGAGACGTGC 277 35 926 Antisense
Sequence Source Affymetrix Proprietary Database